Publications

Are you planning to publish a paper involving microscopy ?

You have the possibility to contact the microscopists and/or image analysts in our facility.

The BIOP staff is happy to guide you into following the FAIR principles and provide feedback about your Image Acquisition, Processing, Analysis and Visualization.

Furthermore the BIOP staff can :

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

Moreover, this provides the BIOP with useful insights how its tools and services have contributed to the scientific literature.

How to acknowledge the BIOP in a publication?

The type of acknowledgement depends on the type of work and collaboration we have undertaken. For publications the rules and recommendations layed out in the EPFL compliance guide apply. 

For contributions to a publication which do not fulfill the criteria above, we recommend the following sentence:  

We would like to thank the EPFL BioImaging & Optics Core Facility and in particular [person(s)] for their assistance in [imaging / image processing].

It has been reported recently [1] that imaging methods are often not properly documented in publications.
In case you have a general question regarding Image acquisition, processing, analysis and visualization, or are unsure what to include into your Materials and Methods section, do not hesitate to drop us a line or pass by. We are happy to:

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

[1]  Marqués et al.: Science Forum: Imaging methods are vastly underreported in biomedical research, eLife 2020;9:e55133, doi: 10.7554/eLife.55133, Aug 11, 2020.


Latest Publications

Below you will find recent publications by all members of the BioImaging & Optics Platform.

To find all publications, you may head to InfoScience.

MarrowQuant across Aging and Aplasia: A Digital Pathology Tool for Quantification of Bone Marrow Compartments in Histological Sections

J. Tratwal; I. Bekri; C. Boussema; N. Kunz; R. Sarkis et al. 

2020-11-01. Annual Meeting of the American-Society-for-Bone-and Mineral Research (ASBMR), ELECTR NETWORK, Sep 11-15, 2020. p. 95-95.

T Cell-Mediated Transport of Polymer Nanoparticles across the Blood-Brain Barrier

M. Ayer; M. Schuster; I. Gruber; C. Blatti; E. Kaba et al. 

Advanced Healthcare Materials. 2020-11-25.  p. 2001375. DOI : 10.1002/adhm.202001375.

Hookworms Evade Host Immunity by Secreting a Deoxyribonuclease to Degrade Neutrophil Extracellular Traps

T. Bouchery; M. Moyat; J. Sotillo; S. Silverstein; B. Volpe et al. 

Cell Host & Microbe. 2020-02-12. Vol. 27, num. 2, p. 277-+. DOI : 10.1016/j.chom.2020.01.011.

Open Source Tools for Biological Image Analysis

R. Guiet; O. Burri; A. Seitz 

Computer Optimized Microscopy; Humana Press, 2019. p. 460.

A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex

D. Keller; J. Meystre; R. V. Veettil; O. Burri; R. Guiet et al. 

Frontiers In Neuroanatomy. 2019-08-06. Vol. 13, p. 78. DOI : 10.3389/fnana.2019.00078.

An optimized and validated 384-well plate assay to test platelet function in a high-throughput screening format

A. M. Lima; M. E. Bragina; O. Burri; J. B. Chapalay; F. P. Costa-Fraga et al. 

Platelets. 2019-01-01. Vol. 30, num. 5, p. 563-571. DOI : 10.1080/09537104.2018.1514106.

Development of Sample-Adaptable Holders for Lightsheet Microscopy

T. Laroche; O. Burri; L. K. Dubey; A. Seitz 

Frontiers In Neuroanatomy. 2019-03-08. Vol. 13, p. 26. DOI : 10.3389/fnana.2019.00026.

Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence

M. B. Baghdadi; J. Firmino; K. Soni; B. Evano; D. Di Girolamo et al. 

Cell Stem Cell. 2018-12-06. Vol. 23, num. 6, p. 859-+. DOI : 10.1016/j.stem.2018.09.017.

Podosomes, But not the Maturation status, Determine the Protease-Dependent 3D Migration in human Dendritic cells

C. Cougoule; C. Lastrucci; R. Guiet; R. Mascarau; E. Meunier et al. 

Frontiers In Immunology. 2018-04-30. Vol. 9, p. 846. DOI : 10.3389/fimmu.2018.00846.

Fluorescent Benzothiazinone Analogues Efficiently and Selectively Label Dpre1 in Mycobacteria and Actinobacteria

R. Sommer; J. Neres; J. Piton; N. Dhar; A. van der Sar et al. 

ACS Chemical Biology. 2018-11-01. Vol. 13, num. 11, p. 3184-3192. DOI : 10.1021/acschembio.8b00790.

Conference Posters

You can find our conference posters here in PDF format

ELMI 2017

ELMI 2016